From: Aryan Vahedi-Faridi (
Date: Thu Sep 18 2014 - 14:44:34 CDT


My name is Aryan Vahedi and I am a graduate at Morgan State University in
Baltimore, MD. I have been trying to learn VMD and NAMD as best I can but
still am unable to understand how to set up a simulation with a carbon
nanotube and protein present. Could someone instruct me on the proper
procedure to do this? Here is what I have been able to do so far:

-Created a PSF and PDB for a carbon nanotube made by the nanotube builder
that comes with VMD. (Is this alright? Or do I need to use a program like
'Nanotube Modeler'?)

-Created a PSF and PDB for the protein in question (GFP in this case, also
did it for each chain of GFP)

-Made Solvated (Water Box. 0.2 M NaCl) pdb and psf files respectively for
proteins (have not yet done this for the carbon nanotubes)

I guess my question is do I need to merge the molecules (CNT and loaded
protein) prior to running the simulation? If not, how do I solvate the
molecule so that the water box is applied to both at the same time? It
seems I do not understand the fundamental procedure to use when setting up
a simulation between two molecules such as a protein and carbon nanotube. I
would like to run general tutorial-suggested analysis once the simulation
is complete. I am starting with local resources (6-core Athlon) but should
have access to University computing resources in the future.

Thank you for any help it is greatly appreciated!

Morgan State University